A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples

TY - JOUR

T1 - A nested PCR approach for improved recovery of archaeal 16S rRNA gene fragments from freshwater samples

AU - Vissers, E.W.

AU - Bodelier, P.L.E.

AU - Muyzer, G.

AU - Laanbroek, R.

N1 - Reporting year: 2009 Metis note: 4525;CL; MWE ; ME; file:///L:/Endnotedatabases/NIOOPUB/pdfs/PDFS2009\Vissers_ea_4525.pdf

PY - 2009

Y1 - 2009

N2 - In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel electrophoresis (DGGE) with primer sets 21F–958R and Parch519f–Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared with other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea.

AB - In a survey on the presence of archaea in a number of European lakes, it was found that known archaeal primer sets for PCR were not suited for use in freshwater environment, as some lack selectivity, while others were too selective. A nested PCR was developed for denaturing gradient gel electrophoresis (DGGE) with primer sets 21F–958R and Parch519f–Arch915r, respectively. After sequencing of the DGGE bands obtained by this nested method, 93% of the sequences were of archaeal origin. More diverse archaeal DGGE patterns were found as compared with other PCR methods. The nested PCR-DGGE method presented here is therefore a reliable tool to analyze the archaeal diversity in freshwater habitats, revealing even more widespread diversity of the archaea.

U2 - 10.1111/j.1574-6968.2009.01718.x

DO - 10.1111/j.1574-6968.2009.01718.x

M3 - Article

SN - 0378-1097

VL - 298

SP - 193

EP - 198

JO - FEMS Microbiology Letters

JF - FEMS Microbiology Letters

IS - 2

ER -